Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin

Braffman, Nathaniel R.; Piscotta, Frank J.; Hauver, J.; Campbell, Elizabeth A.; Link, A. James; Darst, Seth A.

doi:10.1073/pnas.1817352116

Cited by 80 publications

(133 citation statements)

References 51 publications

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“…The structure of ubonodin differs from any other characterized lasso peptide with an 18 aa‐long loop region. Although we observed turns in this loop region from our NMR structure calculations, structures of MccJ25 bound to RNAP and the outer membrane receptor FhuA show significant remodeling of the MccJ25 loop region when bound to these proteins (Figure S6). We expect similar or even more drastic changes to the ubonodin loop when bound to its target(s) and transporters.…”

Section: Resultsmentioning

confidence: 79%

“…We suggest that this Tyr/Tyr/Gly motif is an excellent predictor of RNAP‐inhibiting lasso peptides. This idea is supported by the recently published crystal structure of MccJ25 bound to RNAP which shows multiple interactions between these residues (Tyr9, Tyr20, and Gly21 in MccJ25) and the β and β′ subunits of RNAP . Acinetodin and klebsidin, also RNAP inhibitors, share the TyrGly motif at their C termini, though both of these peptides lack a Tyr residue at position 9 .…”

Section: Resultsmentioning

confidence: 79%

“…Though the loop structure of ubonodin is much larger and more complex than previously described lasso peptides, its ring and tail regions share some similarity to those found in microcin J25 (MccJ25) and citrocin (Figures and S6). Both of these peptides are RNAP inhibitors, and a recent crystal structure of MccJ25 bound to RNAP shows that the ring and tail regions of MccJ25 make multiple contacts with the secondary channel of RNAP . Thus we hypothesized that ubonodin would also function as an RNAP inhibitor.…”

Section: Resultsmentioning

confidence: 98%

See 2 more Smart Citations

Discovery of Ubonodin, an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex

et al. 2020

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We report the heterologous expression, structure, and antimicrobial activity of a lasso peptide, ubonodin, encoded in the genome of Burkholderia ubonensis. The topology of ubonodin is unprecedented amongst lasso peptides, with 18 of its 28 amino acids found in the mechanically bonded loop segment. Ubonodin inhibits RNA polymerase in vitro and has potent antimicrobial activity against several pathogenic members of the Burkholderia genus, most notably B. cepacia and B. multivorans, causative agents of lung infections in cystic fibrosis patients.

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Section: Resultsmentioning

confidence: 79%

Section: Resultsmentioning

confidence: 79%

Section: Resultsmentioning

confidence: 98%

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Discovery of Ubonodin, an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex

et al. 2020

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“…We next evaluated effects of five small-molecule RNAP inhibitors that, based on crystal structures, interact with sites on RNAP that include or overlap the TL ( (36). Salinamide A (Sal) interacts with the RNAP bridge-helix N-terminal hinge in a manner that potentially sterically precludes TL closure (31).…”

Section: Tl Closing and Opening Can Provide A Checkpoint For Ntp Compmentioning

confidence: 99%

Closing and opening of the RNA polymerase trigger loop

Mazumder

Lin

Kapanidis

et al. 2019

Preprint

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The RNA polymerase (RNAP) trigger loop (TL) is a mobile structural element of the RNAP active center that, based on crystal structures, has been proposed to cycle between an "unfolded"/"open" state that allows an NTP substrate to enter the active center and a "folded"/"closed" state that holds the NTP substrate in the active center. Here, by quantifying single-molecule fluorescence resonance energy transfer between a first fluorescent probe in the TL and a second fluorescent probe elsewhere in RNAP or in DNA, we detect and characterize TL closing and opening in solution. We show that the TL closes and opens on the millisecond timescale; we show that TL closing and opening provides a checkpoint for NTP complementarity, NTP ribo/deoxyribo identity, and NTP tri/di/monophosphate identity, and serves as a target for inhibitors; and we show that one cycle of TL closing and opening typically occurs in each nucleotide addition cycle in transcription elongation.

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“…This leads to the suggestion that Capistruin-producing Burkholderia species either encode an immunity protein or feature some modification of the target. Capistruin and Microcin J25 biological activity is due to their ability to inhibit RNA polymerase (RNAP), although for Microcin J25, the over-production of reactive oxygen species (ROS) through a possible secondary target has also been suggested [37][38][39]. Microcin J25 and Capistruin share the RNAP secondary channel as their binding site.…”

Section: Capistruinmentioning

confidence: 99%

Do Global Regulators Hold the Key to Production of Bacterial Secondary Metabolites?

Thapa

Grove

2019

Antibiotics

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The emergence of multiple antibiotic resistant bacteria has pushed the available pool of antibiotics to the brink. Bacterial secondary metabolites have long been a valuable resource in the development of antibiotics, and the genus Burkholderia has recently emerged as a source of novel compounds with antibacterial, antifungal, and anti-cancer activities. Genome mining has contributed to the identification of biosynthetic gene clusters, which encode enzymes that are responsible for synthesis of such secondary metabolites. Unfortunately, these large gene clusters generally remain silent or cryptic under normal laboratory settings, which creates a hurdle in identification and isolation of these compounds. Various strategies, such as changes in growth conditions and antibiotic stress, have been applied to elicit the expression of these cryptic gene clusters. Although a number of compounds have been isolated from different Burkholderia species, the mechanisms by which the corresponding gene clusters are regulated remain poorly understood. This review summarizes the activity of well characterized secondary metabolites from Burkholderia species and the role of local regulators in their synthesis, and it highlights recent evidence for the role of global regulators in controlling production of secondary metabolites. We suggest that targeting global regulators holds great promise for the awakening of cryptic gene clusters and for developing better strategies for discovery of novel antibiotics.

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Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin

Cited by 80 publications

References 51 publications

Discovery of Ubonodin, an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex

Discovery of Ubonodin, an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex

Closing and opening of the RNA polymerase trigger loop

Do Global Regulators Hold the Key to Production of Bacterial Secondary Metabolites?

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